This package lets you find features (node Z) of nodes (node Y) that all interact with one node (node X), this is repeated for all nodes in the network. One use case is predicting proteins domains that mediate binding of other proteins to a seed protein. This is done by computing a statistic that can be as simple as count of nodes (Y) with a given feature (Z) among all nodes that interact with node X. Formula interface allows defining any statistic needed. As a next step, a specified number of random networks are generated by permuting XY interactions or both XY and YZ interactions. These random networks are used to calculate calculate an empirical pvalue telling how often the observed stastistic or larger seen in these random networks. Two parallelisation strategies are implemented:  multicore parallel procession using parLapply.  multinode parallel processing on a computing cluster using clustermq package.
Package details 


Author  Vitalii Kleshchevnikov 
Maintainer  Vitalii Kleshchevnikov <[email protected]> 
License  Apache License 2.0 
Version  0.1.0 
Package repository  View on GitHub 
Installation 
Install the latest version of this package by entering the following in R:

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